diff --git a/paimon-core/src/main/java/org/apache/paimon/mergetree/compact/PartialUpdateMergeFunction.java b/paimon-core/src/main/java/org/apache/paimon/mergetree/compact/PartialUpdateMergeFunction.java
index 3b6a89d6640c..2093328b9520 100644
--- a/paimon-core/src/main/java/org/apache/paimon/mergetree/compact/PartialUpdateMergeFunction.java
+++ b/paimon-core/src/main/java/org/apache/paimon/mergetree/compact/PartialUpdateMergeFunction.java
@@ -199,7 +199,7 @@ private void updateWithSequenceGroup(KeyValue kv) {
         Iterator<WrapperWithFieldIndex<FieldAggregator>> aggIter = fieldAggregators.iterator();
         WrapperWithFieldIndex<FieldAggregator> curAgg = aggIter.hasNext() ? aggIter.next() : null;
 
-        boolean[] isEmptySequenceGroup = new boolean[getters.length];
+        boolean[] isProcessedSequenceField = new boolean[getters.length];
         for (int i = 0; i < getters.length; i++) {
             FieldsComparator seqComparator = null;
             if (curComparator != null && curComparator.fieldIndex == i) {
@@ -214,15 +214,13 @@ private void updateWithSequenceGroup(KeyValue kv) {
             }
 
             Object accumulator = row.getField(i);
-            if (seqComparator == null) {
-                Object field = getters[i].getFieldOrNull(kv.value());
-                if (aggregator != null) {
-                    row.setField(i, aggregator.agg(accumulator, field));
-                } else if (field != null) {
-                    row.setField(i, field);
+            if (seqComparator != null) {
+                // Skip if this field has already been processed as part of a sequence group
+                if (isProcessedSequenceField[i]) {
+                    continue;
                 }
-            } else {
-                if (isEmptySequenceGroup(kv, seqComparator, isEmptySequenceGroup)) {
+
+                if (isEmptySequenceGroup(kv, seqComparator, isProcessedSequenceField)) {
                     // skip null sequence group
                     continue;
                 }
@@ -237,6 +235,8 @@ private void updateWithSequenceGroup(KeyValue kv) {
                         for (int fieldIndex : seqComparator.compareFields()) {
                             row.setField(
                                     fieldIndex, getters[fieldIndex].getFieldOrNull(kv.value()));
+                            // Mark these sequence fields as processed
+                            isProcessedSequenceField[fieldIndex] = true;
                         }
                         continue;
                     }
@@ -245,27 +245,28 @@ private void updateWithSequenceGroup(KeyValue kv) {
                 } else if (aggregator != null) {
                     row.setField(i, aggregator.aggReversed(accumulator, field));
                 }
+            } else {
+                Object field = getters[i].getFieldOrNull(kv.value());
+                if (aggregator != null) {
+                    row.setField(i, aggregator.agg(accumulator, field));
+                } else if (field != null) {
+                    row.setField(i, field);
+                }
             }
         }
     }
 
     private boolean isEmptySequenceGroup(
-            KeyValue kv, FieldsComparator comparator, boolean[] isEmptySequenceGroup) {
-
-        // If any flag of the sequence fields is set, it means the sequence group is empty.
-        if (isEmptySequenceGroup[comparator.compareFields()[0]]) {
-            return true;
-        }
-
+            KeyValue kv, FieldsComparator comparator, boolean[] isProcessedSequenceField) {
         for (int fieldIndex : comparator.compareFields()) {
             if (getters[fieldIndex].getFieldOrNull(kv.value()) != null) {
                 return false;
             }
         }
 
-        // Set the flag of all the sequence fields of the sequence group.
+        // Mark these sequence fields as processed
         for (int fieldIndex : comparator.compareFields()) {
-            isEmptySequenceGroup[fieldIndex] = true;
+            isProcessedSequenceField[fieldIndex] = true;
         }
 
         return true;
@@ -280,7 +281,7 @@ private void retractWithSequenceGroup(KeyValue kv) {
         Iterator<WrapperWithFieldIndex<FieldAggregator>> aggIter = fieldAggregators.iterator();
         WrapperWithFieldIndex<FieldAggregator> curAgg = aggIter.hasNext() ? aggIter.next() : null;
 
-        boolean[] isEmptySequenceGroup = new boolean[getters.length];
+        boolean[] isProcessedSequenceField = new boolean[getters.length];
         for (int i = 0; i < getters.length; i++) {
             FieldsComparator seqComparator = null;
             if (curComparator != null && curComparator.fieldIndex == i) {
@@ -295,7 +296,12 @@ private void retractWithSequenceGroup(KeyValue kv) {
             }
 
             if (seqComparator != null) {
-                if (isEmptySequenceGroup(kv, seqComparator, isEmptySequenceGroup)) {
+                // Skip if this field has already been processed as part of a sequence group
+                if (isProcessedSequenceField[i]) {
+                    continue;
+                }
+
+                if (isEmptySequenceGroup(kv, seqComparator, isProcessedSequenceField)) {
                     // skip null sequence group
                     continue;
                 }
@@ -319,6 +325,8 @@ private void retractWithSequenceGroup(KeyValue kv) {
                                     updatedSequenceFields.add(field);
                                 }
                             }
+                            // Mark these sequence fields as processed
+                            isProcessedSequenceField[field] = true;
                         }
                     } else {
                         // retract normal field